I would like to specifically look at CpA dinucleotide methylation (ie. make a bedgraph) like I can with CpG's using Bismark. What is the best way to do this? I think I could run bedGraph2cytosine on the CHH bedgraph then use the 2nd last column of the bedGraph2cytosine output (C-context) to pull out all lines that contain "CA_".
Also just to clarify something something, a CHH file should contain everything in the CpG file + CHG file + other C contexts, or does CHH contain all C contexts excluding CpG and CHG?
Also just to clarify something something, a CHH file should contain everything in the CpG file + CHG file + other C contexts, or does CHH contain all C contexts excluding CpG and CHG?
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